BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238512.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 7,713,584 number of mapped reads = 4,279,865 (55.48%) number of supplementary alignments = 34,779 (0.45%) number of secondary alignments = 0 number of mapped bases = 261,919,242 bp number of sequenced bases = 261,806,977 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,362,181 duplication rate = 21.87% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3604 >>>>>>> ACTG content number of A's = 64,170,923 bp (24.51%) number of C's = 45,771,056 bp (17.48%) number of T's = 87,762,429 bp (33.52%) number of G's = 64,085,315 bp (24.48%) number of N's = 17,254 bp (0.01%) GC percentage = 41.96% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 1,495,209 number of insertions = 17,125 mapped reads with insertion percentage = 0.4% number of deletions = 65,045 mapped reads with deletion percentage = 1.5% homopolymer indels = 42.51% >>>>>>> Coverage mean coverageData = 0.0846X std coverageData = 1.0425X There is a 3.64% of reference with a coverageData >= 1X There is a 1.76% of reference with a coverageData >= 2X There is a 1.06% of reference with a coverageData >= 3X There is a 0.66% of reference with a coverageData >= 4X There is a 0.41% of reference with a coverageData >= 5X There is a 0.26% of reference with a coverageData >= 6X There is a 0.17% of reference with a coverageData >= 7X There is a 0.11% of reference with a coverageData >= 8X There is a 0.08% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 24140604 0.09685273361866568 1.2968508898655675 chr2 243199373 25133542 0.10334542268741786 2.3698806851907177 chr3 198022430 15966985 0.08063220413970276 0.6912063764227833 chr4 191154276 22236495 0.11632747885796706 0.7146714573814277 chr5 180915260 13955808 0.07714002677275537 0.5813705803823688 chr6 171115067 14765925 0.08629237190433967 0.9445318051961541 chr7 159138663 14002886 0.08799172832060302 1.1458025753519994 chr8 146364022 9383272 0.0641091428875875 0.8097229760198325 chr9 141213431 10676303 0.07560401956383313 0.7001564786898882 chr10 135534747 11383733 0.08399125133571836 0.750856925458633 chr11 135006516 8803337 0.06520675639092857 0.6099138412112001 chr12 133851895 15389439 0.11497363559925693 0.7293136831179474 chr13 115169878 6586266 0.057187401032065 0.6163569067918266 chr14 107349540 7656910 0.07132690088844348 0.5722801259597672 chr15 102531392 7798112 0.07605584833959925 0.6919172787738213 chr16 90354753 6710617 0.07426966238289645 0.6138414153893078 chr17 81195210 4438070 0.05465925884051535 0.530944332588975 chr18 78077248 8273904 0.10597074323111388 1.6445052416219288 chr19 59128983 5143120 0.08698137087864338 0.9674976896777878 chr20 63025520 5449597 0.08646651388199574 0.620847204210752 chr21 48129895 3274546 0.06803559409385788 0.5775214334678147 chr22 51304566 4316416 0.08413317442350063 0.6343822042524897 chrMT 16571 134997 8.14658137710458 6.779275768193582 chrX 155270560 14563849 0.09379658964326527 0.6677598051606004 chrY 59373566 1734509 0.02921348870977364 0.5320056433860539